Ok here is the deal, Simple rebuild, something that I have done over and over and over again. Followed the book to the "t" with making sure everything is set correctly, TDC, everything, Checked clearences, all within spec. Checked crank, everything good there. Installed new piston and rings, made sure rings were at their proper position on piston.

Once piston installed, started to put the bike back together. Followed the instructions for the timing, all marks line up properly with the appropriate amount of pins between marks, cams installed at TDC, checked clearences again. Everything matches up to what it was before the rebuild. Go to start it and it wont start. The occasional back fire, but nothing at all. Doesn't feel like it has much compression however I ride 450's and to me nothing feels like it has compression compared to those. Have fuel, have spark, All wires checked and recheck... Still will not fire...

Any ideas?

sounds like u know what your doing. if it was me i would turn off gas lean the bike over to drain carb. pull the plug and kick a few times to clear the cc. dry/clean the plug. then tripple check timing. my 08 when it was stock (brand new) i could kickstart it with my hand. so it's hard to tell compression with the auto-decomp.

Hi, my first post here,introduction to follow but I had to reply to this post as I'm exactly the same situation as the OP.
Was there ever a solution found as I'm at my wits end with this bike.
It's a '05 RMZ250 with a fully refurbished and tested head.

You've not got the ignition timing out 180 degrees have you.
IE firing on the exhaust stroke as opposed compression stroke.

I'm 100% sure I have the timing right.
TDC found,timing marks are lined up,cams installed with both lobes facing out and punch marks and pin count
on the money.
I got a second hand replacement magneto that I was assured was from a '05.
It's a Kokusan FP8053 5108 stamped on the outer surface.
The magnets do look a little odd compared to what I'm seeing for sale on Ebay.
Thinking about buying a new magneto just to be sure.

I got my issue sorted. Bought a complete new stator assy.
Pretty sure it was the crank sensor(pick up) that was causing my problem.